Computer Sciences Commons^™

Big Data And Smart Cities, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Context-Driven Automatic Subgraph Creation For Literature-Based Discovery, Delroy H. Cameron, Ramakanth Kavuluru, Thomas Rindflesch, Amit P. Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider

Kno.e.sis Publications

Background: Literature-based discovery (LBD) is characterized by uncovering hidden associations in non-interacting scientific literature. Prior approaches to LBD include use of: 1) domain expertise and structured background knowledge to manually filter and explore the literature, 2) distributional statistics and graph-theoretic measures to rank interesting connections and 3) heuristics to help eliminate spurious connections. However, manual approaches to LBD are not scalable and purely distributional approaches may not be sufficient to obtain insights into the meaning of poorly understood associations. While several graph-based approaches have the potential to elucidate associations, their effectiveness has not been fully demonstrated. A considerable degree of …

Computational Development For Secondary Structure Detection From Three-Dimensional Images Of Cryo-Electron Microscopy, Dong Si

Computer Science Theses & Dissertations

Electron cryo-microscopy (cryo-EM) as a cutting edge technology has carved a niche for itself in the study of large-scale protein complex. Although the protein backbone of complexes cannot be derived directly from the medium resolution (5-10 Å) of amino acids from three-dimensional (3D) density images, secondary structure elements (SSEs) such as alpha-helices and beta-sheets can still be detected. The accuracy of SSE detection from the volumetric protein density images is critical for ab initio backbone structure derivation in cryo-EM. So far it is challenging to detect the SSEs automatically and accurately from the density images at these resolutions. This dissertation …

Smart Data - How You And I Will Exploit Big Data For Personalized Digital Health And Many Other Activities, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

On Using Synthetic Social Media Stimuli In An Emergency Preparedness Functional Exercise, Andrew Hampton, Shreyansh Bhatt, Gary Alan Smith, Jeremy S. Brunn, Hemant Purohit, Valerie L. Shalin, John M. Flach, Amit P. Sheth

Kno.e.sis Publications

This paper details the creation and use of a massive (over 32,000 messages) artificially constructed 'Twitter' microblog stream for a regional emergency preparedness functional exercise. By combining microblog conversion, manual production, and a control set, we created a web based information stream providing valid, misleading, and irrelevant information to public information officers (PIOs) representing hospitals, fire departments, the local Red Cross, and city and county government officials. PIOs searched, monitored, and (through conventional channels) verified potentially actionable information that could then be redistributed through a personalized screen name. Our case study of a key PIO reveals several capabilities that social …

Rice And Mouse Quantitative Phenotype Prediction In Genome-Wide Association Studies With Support Vector Regression, Abdulrhman Fahad M. Aljouie

Theses

Quantitative phenotypes prediction from genotype data is significant for pathogenesis, crop yields, and immunity tests. The scientific community conducted many studies to find unobserved quantitative phenotype high predictive ability models. Early genome-wide association studies (GWAS) focused on genetic variants that are associated with disease or phenotype, however, these variants manly covers small portion of the whole genetic variance, and therefore, the effectiveness of predictions obtained using this information may possibly be circumscribed [ 1 ].

Instead, this study shows prediction ability from whole genome single nucleotide polymorphisms (SNPs) data of 1940 genotyped stoke mouse with - 12k SNPs, and 413 …

Cancer Risk Prediction With Next Generation Sequencing Data Using Machine Learning, Nihir Patel

Theses

The use of computational biology for next generation sequencing (NGS) analysis is rapidly increasing in genomics research. However, the effectiveness of NGS data to predict disease abundance is yet unclear. This research investigates the problem in the whole exome NGS data of the chronic lymphocytic leukemia (CLL) available at dbGaP. Initially, raw reads from samples are aligned to the human reference genome using burrows wheeler aligner. From the samples, structural variants, namely, Single Nucleotide Polymorphism (SNP) and Insertion Deletion (INDEL) are identified and are filtered using SAMtools as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are …

Gender-Based Violence In 140 Characters Or Fewer: A #Bigdata Case Study Of Twitter, Hemant Purohit, Tanvi Banerjee, Andrew Hampton, Valerie L. Shalin, Nayanesh Bhandutia, Amit P. Sheth

Kno.e.sis Publications

Public institutions are increasingly reliant on data from social media sites to measure public attitude and provide timely public engagement. Such reliance includes the exploration of public views on important social issues such as gender-based violence (GBV). In this study, we examine big (social) data consisting of nearly fourteen million tweets collected from Twitter over a period of ten months to analyze public opinion regarding GBV, highlighting the nature of tweeting practices by geographical location and gender. We demonstrate the utility of Computational Social Science to mine insight from the corpus while accounting for the influence of both transient events …

Knowledge Enabled Approach To Predict The Location Of Twitter Users, Revathy Krishnamurthy, Pavan Kapanipathi, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

Knowledge bases have been used to improve performance in applications ranging from web search and event detection to entity recognition and disambiguation. More recently, knowledge bases have been used to analyze social data. A key challenge in social data analysis has been the identification of the geographic location of online users in a social network such as Twitter. Existing approaches to predict the location of users, based on their tweets, rely solely on social media features or probabilistic language models. These approaches are supervised and require large training dataset of geo-tagged tweets to build their models. As most Twitter users …

Mining Behavior Of Citizen Sensor Communities To Improve Cooperation With Organizational Actors, Hemant Purohit

Kno.e.sis Publications

Web 2.0 (social media) provides a natural platform for dynamic emergence of citizen (as) sensor communities, where the citizens generate content for sharing information and engaging in discussions. Such a citizen sensor community (CSC) has stated or implied goals that are helpful in the work of formal organizations, such as an emergency management unit, for prioritizing their response needs. This research addresses questions related to design of a cooperative system of organizations and citizens in CSC. Prior research by social scientists in a limited offline and online environment has provided a foundation for research on cooperative behavior challenges, including ‘ …

Value Oriented Big Data Processing With Applications, Krishnaprasad Thirunarayan

Kno.e.sis Publications

We discuss the nature of Big Data and address the role of semantics in analyzing and processing Big Data that arises in the context of Physical-Cyber-Social Systems. To handle Volume, we advocate semantic perception that can convert low-level observational data to higher-level abstractions more suitable for decision- making. To handle Variety, we resort to semantic models and annotations of data so that intelligent processing can be done independent of heterogeneity of data formats and media. To handle Velocity, we seek to use continuous semantics capability to dynamically create event or situation specific models and recognize relevant new concepts, entities and …

Extracting City Traffic Events From Social Streams, Pramod Anantharam, Payam Barnaghi, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Cities are composed of complex systems with physical, cyber, and social components. Current works on extracting and understanding city events mainly rely on technology enabled infrastructure to observe and record events. In this work, we propose an approach to leverage citizen observations of various city systems and services such as traffic, public transport, water supply, weather, sewage, and public safety as a source of city events. We investigate the feasibility of using such textual streams for extracting city events from annotated text. We formalize the problem of annotating social streams such as microblogs as a sequence labeling problem. We present …

Understanding Social Effects In Online Networks, Huda Alhazmi, Swapna S. Gokhale, Derek Doran

Kno.e.sis Publications

Understanding the motives behind people’s interactions online can offer sound bases to predict how a social network may evolve and also support a host of applications. We hypothesize that three offline social factors, namely, stature, relationship strength, and egocentricity may also play an important role in driving users’ interactions online. Therefore, we study the influence of these three social factors in online interactions by analyzing the transitivity in triads or three-way relationships among users. Analyzing transitivity through the lens of triad census for four popular social networks, namely, Facebook, Twitter, YouTube and Slashdot, we find that: (i) users’ interactions are …

Semantic Gateway As A Service Architecture For Iot Interoperability, Pratikkumar Desai, Amit P. Sheth, Pramod Anantharam

Kno.e.sis Publications

The Internet of Things (IoT) is set to occupy a substantial component of future Internet. The IoT connects sensors and devices that record physical observations to applications and services of the Internet. As a successor to technologies such as RFID and Wireless Sensor Networks (WSN), the IoT has stumbled into vertical silos of proprietary systems, providing little or no interoperability with similar systems. As the IoT represents future state of the Internet, an intelligent and scalable architecture is required to provide connectivity between these silos, enabling discovery of physical sensors and interpretation of messages between things. This paper proposes a …

Knowledge-Driven Personalized Contextual Mhealth Service For Asthma Management In Children, Pramod Anantharam, Tanvi Banerjee, Amit P. Sheth, Krishnaprasad Thirunarayan, Surendra Marupudi, Vaikunth Sridharan

Kno.e.sis Publications

Wide adoption of smartphones and availability of low-cost sensors has resulted in seamless and continuous monitoring of physiology, environment, and public health notifications. However, personalized digital health and patient empowerment can become a reality only if the complex multisensory and multimodal data is processed within the patient context. Contextual processing of patient data along with personalized medical knowledge can lead to actionable information for better and timely decisions. We present a system called kHealth capable of aggregating multisensory and multimodal data from sensors (passive sensing) and answers to questionnaire (active sensing) from patients with asthma. We present our preliminary data …

Using Ehrs For Heart Failure Therapy Recommendation Using Multidimensional Patient Similarity Analytics, Maryam Panahiazar, Vahid Taslimitehrani, Naveen L. Pereira, Jyotishman Pathak

Kno.e.sis Publications

Electronic Health Records (EHRs) contain a wealth of information about an individual patient’s diagnosis, treatment and health outcomes. This information can be leveraged effectively to identify patients who are similar to each for disease diagnosis and prognosis. In recent years, several machine learning methods 1 have been proposed to assessing patient similarity, although the techniques have primarily focused on the use of patient diagnoses data from EHRs for the learning task. In this study, we develop a multidimensional patient similarity assessment technique that leverages multiple types of information from the EHR and predicts a medication plan for each new patient …

Bioinformatics And Biomedical Engineering, Francisco Ortuño, Ignacio Rojas, Kathryn Dempsey Cooper, Sachin Pawaskar, Hesham Ali

Faculty Books and Monographs

Editors: Francisco Ortuño, Ignacio Rojas

Chapter, Identification of Biologically Significant Elements Using Correlation Networks in High Performance Computing Environments, co-authored by Kathryn Dempsey Cooper, Sachin Pawaskar, and Hesham Ali, UNO faculty members.

The two volume set LNCS 9043 and 9044 constitutes the refereed proceedings of the Third International Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, held in Granada, Spain in April 2015. The 134 papers presented were carefully reviewed and selected from 268 submissions. The scope of the conference spans the following areas: bioinformatics for healthcare and diseases, biomedical engineering, biomedical image analysis, biomedical signal analysis, computational genomics, computational …

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We …

Applications Of Machine Learning In Biology And Medicine, Saied Haidarian Shahri

Wayne State University Dissertations

Machine learning as a field is defined to be the set of computational algorithms that improve their performance by assimilating data.

As such, the field as a whole has found applications in many diverse disciplines from robotics and communication in engineering to economics and finance, and also biology and medicine.

It should not come as a surprise that many popular methods in use today have completely different origins.

Despite this heterogeneity, different methods can be divided into standard tasks, such as supervised, unsupervised, semi-supervised and reinforcement learning.

Although machine learning as a field can be formalized as methods trying to …

Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi

Wayne State University Dissertations

Recent progress in DNA amplification techniques, particularly multiple displacement

amplification (MDA), has made it possible to sequence and assemble bacterial

genomes from a single cell. However, the quality of single cell genome assembly has

not yet reached the quality of normal multi-cell genome assembly due to the coverage

bias (including uneven depth of coverage and region blackout) and errors caused by

MDA. Computational methods try to mitigates the amplification bias. In this document

we introduce a de novo co-assembly method using colored de Bruijn graph,

which can overcome the problem of blackout regions due to amplification bias. The

algorithm is …

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Bioinformatics Faculty Publications

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao

Theses and Dissertations

Curiosity of human nature drives us to explore the origins of what makes each of us different. From ancient legends and mythology, Mendel's law, Punnett square to modern genetic research, we carry on this old but eternal question. Thanks to technological revolution, today's scientists try to answer this question using easily measurable gene expression and other profiling data. However, the exploration can easily get lost in the data of growing volume, dimension, noise and complexity. This dissertation is aimed at developing new machine learning methods that take data from different classes as input, augment them with knowledge of feature relationships, …

Anonymized Video Analysis Methods And Systems, Marjorie Skubic, James M. Keller, Fang Wang, Derek T. Anderson, Erik Stone, Robert H. Luke Iii, Tanvi Banerjee, Marilyn J. Rantz

Kno.e.sis Publications

Methods and systems for anonymized video analysis are described. In one embodiment, a first silhouette image of a person in a living unit may be accessed. The first silhouette image may be based on a first video signal recorded by a first video camera. A second silhouette image of the person in the living unit may be accessed. The second silhouette image may be of a different view of the person than the first silhouette image. The second silhouette image may be based on a second video signal recorded by a second video camera. A three-dimensional model of the person …

Protecting Web Servers From Web Robot Traffic, Derek Doran

Kno.e.sis Publications

No abstract provided.

Triad-Based Role Discovery For Large Social Systems, Derek Doran

Kno.e.sis Publications

The social role of a participant in a social system conceptualizes the circumstances under which she chooses to interact with others, making their discovery and analysis important for theoretical and practical purposes. In this paper, we propose a methodology to detect such roles by utilizing the conditional triad censuses of ego-networks. These censuses are a promising tool for social role extraction because they capture the degree to which basic social forces push upon a user to interact with others in a system. Clusters of triad censuses, inferred from network samples that preserve local structural properties, define the social roles. The …

Discovering Perceptions In Online Social Media: A Probabilistic Approach, Derek Doran, Swapna S. Gokhale, Aldo Dagnino

Kno.e.sis Publications

People across the world habitually turn to online social media to share their experiences, thoughts, ideas, and opinions as they go about their daily lives. These posts collectively contain a wealth of insights into how masses perceive their surroundings. Therefore, extracting people’s perceptions from social media posts can provide valuable information about pertinent issues such as public transportation, emergency conditions, and even reactions to political actions or other activities. This paper proposes a novel approach to extract such perceptions from a corpus of social media posts originating from a given broad geographical region. The approach divides the broad region into …

Online Information Searching For Cardiovascular Diseases: An Analysis Of Mayo Clinic Search Query Logs, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak

Kno.e.sis Publications

Since the early 2000’s, Internet usage for health information searching has increased significantly. Studying search queries can help us to understand users “information need” and how do they formulate search queries (“expression of information need”). Although cardiovascular diseases (CVD) affect a large percentage of the population, few studies have investigated how and what users search for CVD. We address this knowledge gap in the community by analyzing a large corpus of 10 million CVD related search queries from MayoClinic.com. Using UMLS MetaMap and UMLS semantic types/concepts, we developed a rule-based approach to categorize the queries into 14 health categories. We …

An Analysis Of Mayo Clinic Search Query Logs For Cardiovascular Diseases, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak

Kno.e.sis Publications

Increasingly, individuals are taking active participation in learning and managing their health by leveraging online resources. Understanding online health information searching behavior can help us to study what health topics users search for and how search queries are formulated. In this work, we analyzed 10 million cardiovascular diseases (CVD) related search queries from MayoClinic.com. We performed semantic analysis on the queries using UMLS MetaMap and analyzed structural and textual properties as well as linguistic characteristics of the queries.

Data Analytics For Power Utility Storm Planning, Lan Lin, Aldo Dagnino, Derek Doran, Swapna S. Gokhale

Kno.e.sis Publications

As the world population grows, recent climatic changes seem to bring powerful storms to populated areas. The impact of these storms on utility services is devastating. Hurricane Sandy is a recent example of the enormous damages that storms can inflict on infrastructure, society, and the economy. Quick response to these emergencies represents a big challenge to electric power utilities. Traditionally utilities develop preparedness plans for storm emergency situations based on the experience of utility experts and with limited use of historical data. With the advent of the Smart Grid, utilities are incorporating automation and sensing technologies in their grids and …

Evaluation Of Microarray-Based Dna Methylation Measurement Using Technical Replicates: The Atherosclerosis Risk In Communities (Aric) Study, Maitreyee Bose, Chong Wu, James S. Pankow, Ellen W. Demerath, Jan Bressler, Myriam Fornage, Megan L. Grove, Thomas H. Mosley, Chindo Hicks, Kari North, Wen Hong Kao, Yu Zhang, Eric Boerwinkle, Weihua Guan

Computer Science Faculty Publications

Background: DNA methylation is a widely studied epigenetic phenomenon; alterations in methylation patterns influence human phenotypes and risk of disease. As part of the Atherosclerosis Risk in Communities (ARIC) study, the Illumina Infinium HumanMethylation450 (HM450) BeadChip was used to measure DNA methylation in peripheral blood obtained from ~3000 African American study participants. Over 480,000 cytosine-guanine (CpG) dinucleotide sites were surveyed on the HM450 BeadChip. To evaluate the impact of technical variation, 265 technical replicates from 130 participants were included in the study.

Results: For each CpG site, we calculated the intraclass correlation coefficient (ICC) to compare variation of methylation levels …